6B2L | pdb_00006b2l

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with piperidin-2-Imine

PDB DOI: https://doi.org/10.2210/pdb6B2L/pdb

Classification: TRANSFERASE
Organism(s): Schistosoma mansoni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-20 Released: 2018-09-26
Deposition Author(s): Faheem, M., Neto, J.B., Collins, P., Pearce, N.M., Valadares, N.F., Bird, L., Pereira, H.M., Delft, F.V., Barbosa, J.A.R.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with piperidin-2-Imine

Faheem, M., Neto, J.B., Collins, P., Pearce, N.M., Valadares, N.F., Bird, L., Pereira, H.M., Delft, F.V., Barbosa, J.A.R.G.

To be published.

Macromolecule Content

Total Structure Weight: 32.08 kDa
Atom Count: 2,368
Modeled Residue Count: 281
Deposited Residue Count: 287
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	287	Schistosoma mansoni	Mutation(s): 0 EC: 2.4.2.1
UniProt
Find proteins for A0A0U3AGT1 (Schistosoma mansoni) Explore A0A0U3AGT1 Go to UniProtKB: A0A0U3AGT1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U3AGT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2IM (Subject of Investigation/LOI) Query on 2IM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PIPERIDIN-2-IMINE C₅ H₁₀ N₂ DHGUMNJVFYRSIG-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.195 (Depositor), 0.198 (DCC)
R-Value Work: 0.171 (Depositor), 0.177 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.74	α = 90
b = 99.74	β = 90
c = 99.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Coot	model building
PHENIX	phasing
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Valadares, N.F.

Barbosa, J.A.R.G.

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.